A tentative schedule of things we will do over the first few weeks. Researcher's Names:
Aldo, Andrew, Michael, Daniel, Janice, Max, Urvashi, Alex, Kaarthik, Aakash
Rishi, Sam, Paul, Priya
NOTE - see bottom of page for previous weeks' schedules and things to catch up on.
This Week
MONDAY 30-Jul
2:30 - Lab Group Meeting/Journal Club (in WELCH classroom)
Final Summer Research Presentations (upload to Google Docs by Sunday night)
2-3 slides, ~ 7 minutes
What your disease and protein target are (since the rest of the group doesn't know exactly what you are working on)
Specifics about size of gene, GC% content, etc.
Size of protein, is there a structure in the PDB?
What you set out to do
Where you have gotten so far (show gel pics, images, graphs or relevant data)
Challenges, failures, side-steps
Future Directions (i.e. Fall semester and beyond)
Social ???
TUESDAY 31-Jul
WEDNESDAY 1-Aug
THURSDAY 2-Aug
Dr. B - out of town
FRIDAY 3-Aug
Dr. B - out of town
(Remember to work on your 1 page (~500) word summary of your research. No figures needed.
- Motivation, What you did, What you have left to do on your project. Reflect on what you have gotten out of your summer research and if it was what you expected.
- submit to Dr. B before Sept. 1st. Then I will proof and send to Dr. Simmons.
SATURDAY 4-Aug
Dr. B - out of town
SUNDAY 5-Aug
Dr. B - out of town....
Next Week
FRIDAY - August 10thLast Day of VDS Summer Research
Transformation of plasmids to make stocks - pUC19
(NOT YET) ProtocolBacterialGrowthCurve_VDS_Summ12.xlsx - test (needs to be modified a little)
Staff Stuff:
Label new reagents and supplies
Dilute new 100 bp ladder in Blue Juice + TE
test all tubes of [[#|Taq Polymerase]] in PCR
Target Discovery choices --> order primer sets
ToDo List:
Journal Club
Lab Notebook Checks
Protocol cost analysis (Transformation, cloning)
Walk through protein expression (use current mentor's enzymes)
Joey & Christina's Francisella HAP enzyme
Sadhana's M. tuberculosis enzyme
Joshua's M. tuberculosis enzyme
J.C.'s YopH
Lab Safety training
- New guys - walk through with Dr. B
- everyone else - complete 2 new Lab Safety classes - see Required Lab Safety link on the left hand side menu of this page
Paper copy of safety [[#|training]] to Dr. B
4 plates of LB with Amp
Make 250 ml of LB
Transform pGBR22 into DH5alpha
Do this after a successful transformation:
Bacterial Growth Curve.xls
Make Amp and Kan stocks (50ug/ul)
4 people: Transform a plasmid for Midi-prep (pGBR22)
rest: Transformation Efficiency
Order 'Tail' Primers for class -
PCR Primer Design for pNIC-Bsa4 Cloning.docx
expression, purification, characterization
test specific activity of your enzyme for lot to lot consistency
Research Presentation Schedule:
Date: Name
Instructions: prepare 3-5 Powerpoint slides to present your work to date
Intro (talk about your disease and what your protein does), Objectives, Methods& Results, Future Directions
make and run SDS-Page protein gels
load and run SDS-Page protein gels
MONDAY 6-Aug
TUESDAY 7-Aug
WEDNESDAY 8-Aug
Week 1
THURSDAY 31-May
1:00 - PAI 2.14 First meeting
Post your class schedule to GDOcs - see Announcements Page
Create your own folder in Google Docs under the folder: /StudentFolders
Protocol Target Discovery
FRIDAY 1-Jun Simultaneously:
Target group meetings with Dr. B - computer lab
'Learn how to submit to DNA sequencing' (starring Joey) - wet lab
Maybe......
SATURDAY 2-Jun SUNDAY 3-Jun
Week 2
MONDAY 4-Jun
12:00 -
Target group meeting with Dr. B (Francisella group - Aldo, Janice, Jennifer R.)
2:30 - 2nd Group Meeting (Location TBA - start in PAI 2.14)
1st Journal Club - Max M.
Target group meetings with Dr. B - Chagas (T. cruzi), Yersinia pestis, , Wolbachia)
Leishmania - work on Primer Design.
Protocol Primer Design OverlapAssembly - con't....
Order Overlap Primers for class - con't....
Print out safety training, hole punch and place in VDS sign in folder under the 'Safety' tab
Returning VDSers - have 2 classes to take
New guys - have lots of classes to take
TUESDAY 5-Jun
1:00 Protocol Primer Design OverlapAssembly - con't....
Order Overlap Primers for class - con't....
Choose a Plasmid to work with on these next 2 exercises(pGBR22 or pGFP or pmCherry)
Nanodrop plasmid DNA (pGBR22 or pGFP or pmCherry)
WEDNESDAY 6-Jun
On Your Targets Page:
Add Link to DNA Works output text file
Add substrate cost, quantity, and catalog numbers (and supplier) for enzyme assay reagents
Add image of BRENDA reaction mechanism (screenshot it)
Check DNA sequence
3:00 - Analyze DNA sequence exercise - in WEL computer lab
THURSDAY 7-Jun
RE Digest
Agarose Gel
Journal article for next week is posted on Journal Club page.
FRIDAY 8-Jun
Safety training check.
Michael - printed out copies of the Journal club article for you to take and read - they are on the front table.
PCR - of pGBR22
Agarose Gel
SATURDAY 9-Jun
SUNDAY 10-Jun
Week 3
complete - Analyze DNA sequence exercise
Safety training check.
MONDAY 11-Jun
Gel check PCR from Friday (pGBR22) - repeat PCR if it failed
Someone order primers (not our gene ones) with Dr. B and Joey.
Dilute some primers
New guys
- pipetting exercise and Buffers & Solutions (Lab 1 of Spring VDS)
High Schoolers
- Lab Safety training
- pipetting exercise and Buffers & Solutions (Lab 1 of Spring VDS)
- Literature search assignment
PCR practice
2:30 pm - Lab Group Meeting in WELCH 3.260 (read journal club article prior)
Choose a Plasmid to work with on these next 2 exercises(pGBR22 or pGFP or pmCherry)
Nanodrop plasmid DNA (pGBR22 or pGFP or pmCherry)
Transformation Efficiency Protocol (pGBR22 or pGFP or pmCherry)
PCR practice
Repeat 1st PCR if failed (why did it fail?)
Then:
ProtocolPCRforREcloningGREEN.xls OR ProtocolPCRforREcloningRED.xls
PM - 4 people transform pNIC-Bsa4 in DH5alpha
PM - 4 people transform YopH and or PTP1b for protein expression practice (or do Ft Hap, Mt PSTP, etc)
Someone transform pmCherry for their Transformation Efficiency lab - Rishi and Jennifer?
High Schoolers & Newer people
- Lab Safety training
- make Google Docs folders in StudentFolders
- Nanodrop protocol
- Submit to DNA Sequencing protocol
- pipetting exercise and Buffers & Solutions (Lab 1 of Spring VDS)
- Literature search assignment
WEDNESDAY 13-Jun PCR - practice -
ProtocolPCRforREcloningGREEN.xls OR ProtocolPCRforREcloningRED.xls
?? Protein Expression practice (YopH, PTP1b, Ft HAP, MtPSTP, MtPTPb) - takes ALL day
PCR practice
check pNIC-Bsa4 transformation plates
grow up pNIC-Bsa4 o/n (overnight)
grow up YopH and or PTP1b for protein expression practice
High Schoolers & Newer people
- pipetting exercise and Buffers & Solutions (Lab 1 of Spring VDS)
- Literature search assignment
- Analyze DNA Sequence exercise
THURSDAY 14-Jun
Order: 500ml flask clamps, 4L flasks and 4L flask clamps
Store overnight LB flasks in Fridge or go straight to 1st spin down step of MidiPrep (can save pellet in freezer until afternoon)
Someone transform pmCherry and pGFP for their Transformation Efficiency lab - Rishi and Jennifer? Paul, Urvashi
?grow up pmCherry and pGFP o/n (overnight) - Urvashi, Rishi, Jennnifer, Andrew, Kaarthik
High Schoolers & Newer people
- pipetting exercise and Buffers & Solutions (Lab 1 of Spring VDS)
- Literature search assignment
- Analyze DNA Sequence exercise
- RE digest
FRIDAY 15-Jun
Order: 500ml flask clamps, and 4L flask clamps
LARRY - test all tubes of KOD Polymerases in PCR
For those listed on board:
Pick up primers we ordered 2 days ago
ProtocolPrimerDilutionVDS_Summ12.docx
PCRs to do:
ProtocolPCRforREcloningGREEN.xls OR ProtocolPCRforREcloningRED.xls
ProtocolPCR_pLICsequencing.xls
Spin down and then Midi-prep pNIC-Bsa4 (in pairs) -
Everyone: ProtocolDNASequencingFacilitypNIC-Bsa4_VDS_Summ12.doc (if you did not do on Friday)
PCRs to do succesfully before you can move on to Target cloning:
ProtocolPCRforREcloningGREEN.xls OR ProtocolPCRforREcloningRED.xls
ProtocolPCR_pLICsequencing.xls
Veteran VDSers:
Pick up target tail primers (Leader and Laggers) we ordered 2 days ago (Joey to get in MBB building)
ProtocolPrimerDilutionVDS_Summ12.docx
Make your Oligo Mixfor your target (first step in Overlap PCR protocol) using PLATE of overlap primers - VERY important to not cross-contaminate your primers!!
ProtocolPCR_PrimerOverlapVDS_Summ12.docx
takes A LONG time to thaw primers in box.
Transformation Efficiency: pmCherry Rishi,Faiz, Priya, pGFP Bobbi, Paul, Jennifer
TUESDAY 19-Jun
Dr. B of town
Joey in Ochem Lab
Christina doing Intel internship
- Larry to work with new guys on PyMol Labs 1 & 2 (Rishi, Jennifer R., Sam, Paul, Bobbi, Priya, Faiz)
- Day off for everyone else (Holiday: National Virtual Screening Day!)
6:00 - Lab floors will be getting stripped and waxed. NO ONE IN LAB at this time. Please clean up loose stuff off the floors.
WEDNESDAY 20-Jun
Dr. B of town
Veteran VDSers:
Overlap PCRs
Make Kan/Sucrose LB Agar plates for your target cloning
New guys: Rishi,Faiz, Priya, Bobbi, Paul, Jennifer,
LabBeer'sLawVDS_Spring12.doc (see Google Docs/Protocols/Spring12_Labs/)
Grow up pmCherry and pGFP overnight each in 2 x 80 ml of LB - ,Faiz, Priya, pmCherry - Faiz, Priya, Paul pGFP - Bobbi, Jennifer,
Grow up pNIC-Bsa4 for Midiprep tomorrow in 2x 80 ml of LB: Rishi, Urvashi,
THURSDAY 21-Jun
Veteran VDSers:
Make Kan/Sucrose LB Agar plates for your target cloning
ProtocolPCRforREcloningGREEN.xls OR ProtocolPCRforREcloningRED.xls
Midiprep on pNIC-Bsa4 : Rishi, Urvashi,
After your Primary and Secondary Overlap PCR work, go to : ProtocolpNIC-Bsa4_cloningVDS_Summ12.doc
2:00 - Joey & Dr. B tour the Algae lab
After your Primary and Secondary Overlap PCR work, go to : ProtocolpNIC-Bsa4_cloningVDS_Summ12.doc
Midiprep on pNIC-Bsa4 : Rishi, Urvashi,
Midiprep on pUC19 : ??
Transformation of plasmids to make stocks - pUC19
Grow up pNIC-Bsa4 for Midiprep tomorrow in 2x 80 ml of LB: ??
New guys: Rishi,Faiz, Priya, Bobbi, Paul
Gel Check 1st PCR
LabBeer'sLawVDS_Spring12.doc (see Google Docs/Protocols/Spring12_Labs/)
PyMol 2, 3Literature search assignment
Analyze DNA Sequence exercise
ProtocolPrimerDilutionVDS_Summ12.docx
TUESDAY 26-Jun
Mentors: prepare RE digest products for MSers
(Andrew, Alex, Michael, Daniel) - check on your LB and [[#|Flasks]] for expression
Veteran VDSers - work on cloning
Midiprep on pNIC-Bsa4 : Rishi, Urvashi, Janice
6:00 [[#|start]] overnight culture for protein expression (Andrew, Alex, Michael, Daniel)
Joey & Christina's Francisella HAP enzyme
Sadhana's M. tuberculosis enzyme
WEDNESDAY 27-Jun
10:30 - all day: protein expression (Andrew, Alex, Michael, Daniel)
Joey & Christina's Francisella HAP enzyme
Sadhana's M. tuberculosis enzyme
THURSDAY 28-Jun
Make LB and Autoclave with flasks that you will use.
-- Kaarthik prepare LB and Flasks
------- put 500ml into in 5x 2L flasks
------ put 50 ml into 10 x 250 ml flasks
1:00 - - Urvashi, Janice, Max, Aldo - put LB and flasks in Autoclave (can autoclave directly in flask)
1:00 - Make Protein Gels (Homemade SDS-Page) with Dr. B or Joey - Daniel, Andrew, Alex, Michael
5:00 - Pick colonies and Start o/n protein expression in the 50 ml LB Flaks
For each person:
1. one flask at 37degC in air incubator
2. one flask at 30degC in water bath shaker
Max - MtPSTP (Sadhana's Tuberculosis)
Urvashi - MtPSTP (Sadhana's Tuberculosis)
Kaarthik - FtHAP (Joey's and Christina's Francisella)
Janice - FtHAP (Joey's and Christina's Francisella)
Rishi - FtHAP (Joey's and Christina's Francisella)
5:00 - Janice - grow up some flaks of 2x80ml of LB with pNIC-Bsa4 in Kanamycin for eventual midiprep
Meet at the lab at 5:30 to head over to Dr. B's house
Will use cars or can also take the #21 Bus that leaves from Dean Keeton & University @ 5:47 pm
The Naturally Obsessed viewing will be Thursday June 28th form 6-7 pm at Dr. B's House
FRIDAY 29-Jun
12:30, 1:00 - all day: protein expression (Max , Kaarthik , Urvashi , Janice , Rishi, Aldo (observe) )
-- we will start a little later than we normally would but we will use an abbreviated induction phase (~ 3 hrs) so that we can finish in a more reasonable time.
Monitor log phase growth in Excel spreadsheet graph
Janice - spin down pNIC-Bsa4 pellets. Save for doing Midiprep next week
Make Protein Gels (Homemade SDS-Page) with Dr. B or Joey - Alex, Michael
------------------------------------- (and if time permits: Max, Kaarthik, Uvashi, Janice, Rishi, Aldo)
High Schoolers and new guys
pmCherry PCR
pLIC PCR
EVERYONE: determine gene inside pNIC-Bsa4 by checking your pLIC sequencing that you sent to the core the other week
SATURDAY 30-Jun SUNDAY 1-Jul
(NOT YET) ProtocolBacterialGrowthCurve_VDS_Summ12.xlsx - test (needs to be modified a little)
MONDAY 2-Jul
EVERYONE: determine gene inside pNIC-Bsa4 by checking your pLIC sequencing that you sent to the core the other week
EVERYONE THAT HAS DONE MIDI-Prep (successfully): Have you submitted your sample to sequencing? Does it turn out to be the right plasmid?
Veteran VDSers - work on cloning
Daniel & Andrew - do test growth of FtHAP and MtPSTP in 50 ml of LB + Kan
Each Person:
one flask at 30degC in water bath shaker
one flask at 37deg in air incubator
Measure OD every few hours over ~ 8hrs time span until OD reaches 1.000 at 600nm
Make LB and Autoclave with flasks that you will use.
------- put 500ml into in 2x 2L flasks
------ put 50 ml into 4 x 250 ml flasks
2:30 - Lab Group Meeting/Journal Club (in WELCH classroom)
High Schoolers and new guys (Rishi,Faiz, Priya, Bobbi, Paul):
--ProtocolPrimerDilutionVDS_Summ12.docx
--pmCherry PCR
--pLIC PCR - ProtocolPCR_pLICsequencing.xls
--Overlap PCR of target
Janice - overnight growth of 2x 80ml of LB with pNIC-Bsa4 colonies for doing Midiprep
Make Protein Gels (Homemade SDS-Page) with Dr. B or Joey - Alex, Michael
------------------------------------- (and if time permits: Max, Kaarthik, Uvashi, Janice, Rishi, Aldo
TUESDAY 3-Jul
Janice - spin down samples for pNIC-Bsa4 Midiprep
Protein Sonication (Andrew, Alex, Michael, Daniel)
Protein expression - AGAIN
Joey & Christina's Francisella HAP enzyme
Sadhana's M. tuberculosis enzyme
Monitor log phase growth in Excel spreadsheet graph
make SDS-Page protein gels for characterization step
3:00 - Algae Lab Tour: Meet in PAI 2.14 - then will walk over to BIO 320
Janice and Sam - Midiprep pNIC-Bsa4 plasmid samples, Nanodrop them and then send to sequencing
WEDNESDAY 4-Jul
OFF - Independence Day
THURSDAY 5-Jul
EVERYONE: determine gene inside pNIC-Bsa4 by checking your pLIC sequencing that you sent to the core the other week
EVERYONE THAT HAS DONE MIDI-Prep (successfully): Have you submitted your sample to sequencing? Does it turn out to be the right plasmid?
~ 10:00 Prep Starter Culture (grow until ~ 8hrs to OD600 = 1 )
Max - MtPSTP (Sadhana's Tuberculosis)
Urvashi - MtPSTP (Sadhana's Tuberculosis)
Kaarthik - FtHAP (Joey's and Christina's Francisella)
Janice - FtHAP (Joey's and Christina's Francisella)
Aldo- FtHAP (Joey's and Christina's Francisella)
Protein Expression People also make LB media and autoclave
Protein Sonication (Andrew, Alex, Michael, Daniel)
Janice and Sam - send Midiprep sample of pNIC-Bsa4 to sequencing
~ 6:00 Move Starter Cultureto store in 4degC
Max - MtPSTP (Sadhana's Tuberculosis)
Urvashi - MtPSTP (Sadhana's Tuberculosis)
Kaarthik - FtHAP (Joey's and Christina's Francisella)
Janice - FtHAP (Joey's and Christina's Francisella)
Aldo- FtHAP (Joey's and Christina's Francisella)
FRIDAY 6-Jul
Protein Purification (Andrew, Alex, Michael, Daniel)
--- Run gels, stain and destain
Protein expression 11:00 ? - talk to Dr. B if you can't make this time
Max - MtPSTP (Sadhana's Tuberculosis)
Urvashi - MtPSTP (Sadhana's Tuberculosis)
Kaarthik - FtHAP (Joey's and Christina's Francisella)
Janice - FtHAP (Joey's and Christina's Francisella)
Aldo- FtHAP (Joey's and Christina's Francisella)
make SDS-Page protein gels for characterization step
Researcher's Names:
Aldo, Andrew, Michael, Daniel, Janice, Max, Urvashi, Alex, Kaarthik, Aakash
Rishi, Sam, Paul, Priya
NOTE - see bottom of page for previous weeks' schedules and things to catch up on.
This Week
MONDAY 30-Jul2:30 - Lab Group Meeting/Journal Club (in WELCH classroom)
Final Summer Research Presentations (upload to Google Docs by Sunday night)
Social ???
TUESDAY 31-Jul
WEDNESDAY 1-Aug
THURSDAY 2-Aug
Dr. B - out of town
FRIDAY 3-Aug
Dr. B - out of town
(Remember to work on your 1 page (~500) word summary of your research. No figures needed.
- Motivation, What you did, What you have left to do on your project. Reflect on what you have gotten out of your summer research and if it was what you expected.
- submit to Dr. B before Sept. 1st. Then I will proof and send to Dr. Simmons.
SATURDAY 4-Aug
Dr. B - out of town
SUNDAY 5-Aug
Dr. B - out of town....
Next Week
FRIDAY - August 10thLast Day of VDS Summer Research
Cool Stuff We May Not Get To:
Screening with ICM
- pharmacophore models
Homology ModelingDSF (Differential Scanning Fluorimetry) assays
qPCR
Crystallization trials
Transformation of plasmids to make stocks - pUC19
(NOT YET) ProtocolBacterialGrowthCurve_VDS_Summ12.xlsx - test (needs to be modified a little)
Staff Stuff:
Label new reagents and supplies
Dilute new 100 bp ladder in Blue Juice + TE
test all tubes of [[#|Taq Polymerase]] in PCR
Target Discovery choices --> order primer sets
ToDo List:
Journal Club
Lab Notebook Checks
Protocol cost analysis (Transformation, cloning)
Walk through protein expression (use current mentor's enzymes)
Lab Safety training
- New guys - walk through with Dr. B
- everyone else - complete 2 new Lab Safety classes - see Required Lab Safety link on the left hand side menu of this page
Paper copy of safety [[#|training]] to Dr. B
4 plates of LB with Amp
Make 250 ml of LB
Transform pGBR22 into DH5alpha
Do this after a successful transformation:
Bacterial Growth Curve.xls
Make Amp and Kan stocks (50ug/ul)
4 people: Transform a plasmid for Midi-prep (pGBR22)
rest: Transformation Efficiency
Order 'Tail' Primers for class -
PCR Primer Design for pNIC-Bsa4 Cloning.docx
expression, purification, characterization
Research Presentation Schedule:
Date: Name
Instructions: prepare 3-5 Powerpoint slides to present your work to date
make and run SDS-Page protein gels
load and run SDS-Page protein gels
MONDAY 6-Aug
TUESDAY 7-Aug
WEDNESDAY 8-Aug
Week 1
THURSDAY 31-May1:00 - PAI 2.14 First meeting
Post your class schedule to GDOcs - see Announcements Page
Create your own folder in Google Docs under the folder: /StudentFolders
Protocol Target Discovery
FRIDAY 1-Jun
Simultaneously:
Target group meetings with Dr. B - computer lab
'Learn how to submit to DNA sequencing' (starring Joey) - wet lab
Maybe......
SATURDAY 2-Jun
SUNDAY 3-Jun
Week 2
MONDAY 4-Jun12:00 -
Target group meeting with Dr. B (Francisella group - Aldo, Janice, Jennifer R.)
2:30 - 2nd Group Meeting (Location TBA - start in PAI 2.14)
1st Journal Club - Max M.
Target group meetings with Dr. B - Chagas (T. cruzi), Yersinia pestis, , Wolbachia)
Leishmania - work on Primer Design.
Protocol Primer Design OverlapAssembly - con't....
Order Overlap Primers for class - con't....
Print out safety training, hole punch and place in VDS sign in folder under the 'Safety' tab
TUESDAY 5-Jun
1:00 Protocol Primer Design OverlapAssembly - con't....
Order Overlap Primers for class - con't....
Choose a Plasmid to work with on these next 2 exercises(pGBR22 or pGFP or pmCherry)
WEDNESDAY 6-Jun
On Your Targets Page:
Add Link to DNA Works output text fileAdd substrate cost, quantity, and catalog numbers (and supplier) for enzyme assay reagents
Add image of BRENDA reaction mechanism (screenshot it)
Check DNA sequence
3:00 - Analyze DNA sequence exercise - in WEL computer lab
THURSDAY 7-Jun
RE Digest
Agarose Gel
Journal article for next week is posted on Journal Club page.
FRIDAY 8-Jun
Safety training check.
Michael - printed out copies of the Journal club article for you to take and read - they are on the front table.
PCR - of pGBR22
Agarose Gel
SATURDAY 9-Jun
SUNDAY 10-Jun
Week 3
complete - Analyze DNA sequence exerciseSafety training check.
MONDAY 11-Jun
Gel check PCR from Friday (pGBR22) - repeat PCR if it failed
Someone order primers (not our gene ones) with Dr. B and Joey.
Dilute some primers
New guys
- pipetting exercise and Buffers & Solutions (Lab 1 of Spring VDS)
High Schoolers
- Lab Safety training
- pipetting exercise and Buffers & Solutions (Lab 1 of Spring VDS)
- Literature search assignment
PCR practice
2:30 pm - Lab Group Meeting in WELCH 3.260 (read journal club article prior)
Choose a Plasmid to work with on these next 2 exercises(pGBR22 or pGFP or pmCherry)
TUESDAY 12-Jun
Naturally Obsessed Form - when to watch this documentary- Please fill out this form....
https://docs.google.com/spreadsheet/viewform?formkey=dGdJaEQ5cUtEQm1uaXJ5LVNNdUR4NkE6MQ
Check Transformation Efficiency
PCR practice
Repeat 1st PCR if failed (why did it fail?)
Then:
ProtocolPCRforREcloningGREEN.xls OR ProtocolPCRforREcloningRED.xls
PM - 4 people transform pNIC-Bsa4 in DH5alpha
PM - 4 people transform YopH and or PTP1b for protein expression practice (or do Ft Hap, Mt PSTP, etc)
Someone transform pmCherry for their Transformation Efficiency lab - Rishi and Jennifer?
High Schoolers & Newer people
- Lab Safety training
- make Google Docs folders in StudentFolders
- Nanodrop protocol
- Submit to DNA Sequencing protocol
- pipetting exercise and Buffers & Solutions (Lab 1 of Spring VDS)
- Literature search assignment
WEDNESDAY 13-Jun
PCR - practice -
ProtocolPCRforREcloningGREEN.xls OR ProtocolPCRforREcloningRED.xls
?? Protein Expression practice (YopH, PTP1b, Ft HAP, MtPSTP, MtPTPb) - takes ALL day
PCR practice
check pNIC-Bsa4 transformation plates
grow up pNIC-Bsa4 o/n (overnight)
grow up YopH and or PTP1b for protein expression practice
High Schoolers & Newer people
- pipetting exercise and Buffers & Solutions (Lab 1 of Spring VDS)
- Literature search assignment
- Analyze DNA Sequence exercise
THURSDAY 14-Jun
Order: 500ml flask clamps, 4L flasks and 4L flask clamps
Store overnight LB flasks in Fridge or go straight to 1st spin down step of MidiPrep (can save pellet in freezer until afternoon)
1:00 Everyone:
PCRs to do:
ProtocolPCRforREcloningGREEN.xls OR ProtocolPCRforREcloningRED.xls
ProtocolPCR_pLICsequencing.xls
Spin down and then Midi-prep pNIC-Bsa4 (in pairs) -
Everyone: ProtocolDNASequencingFacilitypNIC-Bsa4_VDS_Summ12.doc
Someone transform pmCherry and pGFP for their Transformation Efficiency lab - Rishi and Jennifer? Paul, Urvashi
?grow up pmCherry and pGFP o/n (overnight) - Urvashi, Rishi, Jennnifer, Andrew, Kaarthik
High Schoolers & Newer people
- pipetting exercise and Buffers & Solutions (Lab 1 of Spring VDS)
- Literature search assignment
- Analyze DNA Sequence exercise
- RE digest
FRIDAY 15-Jun
Order: 500ml flask clamps, and 4L flask clamps
LARRY - test all tubes of KOD Polymerases in PCR
For those listed on board:
PCRs to do:
ProtocolPCRforREcloningGREEN.xls OR ProtocolPCRforREcloningRED.xls
ProtocolPCR_pLICsequencing.xls
Spin down and then Midi-prep pNIC-Bsa4 (in pairs) -
Everyone: ProtocolDNASequencingFacilitypNIC-Bsa4_VDS_Summ12.doc
High Schoolers & Newer people
- Literature search assignment
- Analyze DNA Sequence exercise
- RE digest check on Gel
SATURDAY 16-Jun
SUNDAY 17-Jun
Dr. B of town
Week 4
MONDAY 18-JunDr. B of town
This is what Dr. B is doing:
http://workshop.eupathdb.org/2012/index.php?page=schedule
Everyone: ProtocolDNASequencingFacilitypNIC-Bsa4_VDS_Summ12.doc (if you did not do on Friday)
PCRs to do succesfully before you can move on to Target cloning:
ProtocolPCRforREcloningGREEN.xls OR ProtocolPCRforREcloningRED.xls
ProtocolPCR_pLICsequencing.xls
Veteran VDSers:
Transformation Efficiency:
pmCherry Rishi,Faiz, Priya,
pGFP Bobbi, Paul, Jennifer
TUESDAY 19-Jun
Dr. B of town
Joey in Ochem Lab
Christina doing Intel internship
- Larry to work with new guys on PyMol Labs 1 & 2 (Rishi, Jennifer R., Sam, Paul, Bobbi, Priya, Faiz)
- Day off for everyone else (Holiday: National Virtual Screening Day!)
6:00 - Lab floors will be getting stripped and waxed. NO ONE IN LAB at this time. Please clean up loose stuff off the floors.
WEDNESDAY 20-Jun
Dr. B of town
Veteran VDSers:
- Overlap PCRs
- Make Kan/Sucrose LB Agar plates for your target cloning
New guys: Rishi,Faiz, Priya, Bobbi, Paul, Jennifer,- LabBeer'sLawVDS_Spring12.doc (see Google Docs/Protocols/Spring12_Labs/)
Grow up pmCherry and pGFP overnight each in 2 x 80 ml of LB - ,Faiz, Priya,pmCherry - Faiz, Priya, Paul
pGFP - Bobbi, Jennifer,
Grow up pNIC-Bsa4 for Midiprep tomorrow in 2x 80 ml of LB: Rishi, Urvashi,
THURSDAY 21-Jun
Veteran VDSers:
ProtocolMidiPrepKit_HiSpeed_VDS.doc on
pmCherry - Faiz, Priya, Paul
pGFP - Bobbi, Jennifer,
pNIC-Bsa4 : Rishi, Urvashi,
Grow up pNIC-Bsa4 for Midiprep tomorrow in 2x 80 ml of LB: ????, ????
Grow up pGFP
FRIDAY 22-Jun
(NOT YET) ProtocolBacterialGrowthCurve_VDS_Summ12.xlsx - test (needs to be modified a little)
Veteran VDSers:
Midiprep on pNIC-Bsa4 : Rishi, Urvashi,
After your Primary and Secondary Overlap PCR work, go to : ProtocolpNIC-Bsa4_cloningVDS_Summ12.doc
2:00 - Joey & Dr. B tour the Algae lab
SATURDAY 23-Jun
SUNDAY 24-Jun
5th Week
Naturally Obsessed viewingNaturally Obsessed Form 2 - when to watch this documentary- Please [[#|fill out]] this form.... for the SECOND time!
https://docs.google.com/spreadsheet/viewform?formkey=dHp6M2hkcE16RlRLcW1wcHNPTXp3Vmc6MA
The Naturally Obsessed viewing will be Thursday June 28th form 6-7 pm ?? at Dr. B's House
Fill out - Medical Waiver (only 1 per person)
Fill out - 2 Liability forms:
Walk through protein expression (use current mentor's enzymes)
make SDS-Page protein gels for characterization step
MONDAY 25-Jun
2:30 - Lab Group Meeting in WELCH with Journal Club
Veteran VDSers:
Midiprep on pNIC-Bsa4 : Rishi, Urvashi,
Midiprep on pUC19 : ??
Transformation of plasmids to make stocks - pUC19
Grow up pNIC-Bsa4 for Midiprep tomorrow in 2x 80 ml of LB: ??
New guys: Rishi,Faiz, Priya, Bobbi, Paul
- Gel Check 1st PCR
- LabBeer'sLawVDS_Spring12.doc (see Google Docs/Protocols/Spring12_Labs/)
- PyMol 2, 3Literature search assignment
ProtocolPrimerDilutionVDS_Summ12.docxAnalyze DNA Sequence exercise
TUESDAY 26-Jun
Mentors: prepare RE digest products for MSers
(Andrew, Alex, Michael, Daniel) - check on your LB and [[#|Flasks]] for expression
Veteran VDSers - work on cloning
Midiprep on pNIC-Bsa4 : Rishi, Urvashi, Janice
6:00 [[#|start]] overnight culture for protein expression (Andrew, Alex, Michael, Daniel)
WEDNESDAY 27-Jun
10:30 - all day: protein expression (Andrew, Alex, Michael, Daniel)
THURSDAY 28-Jun
Make LB and Autoclave with flasks that you will use.
-- Kaarthik prepare LB and Flasks
------- put 500ml into in 5x 2L flasks
------ put 50 ml into 10 x 250 ml flasks
1:00 - - Urvashi, Janice, Max, Aldo - put LB and flasks in Autoclave (can autoclave directly in flask)
1:00 - Make Protein Gels (Homemade SDS-Page) with Dr. B or Joey - Daniel, Andrew, Alex, Michael
5:00 - Pick colonies and Start o/n protein expression in the 50 ml LB Flaks
For each person:
1. one flask at 37degC in air incubator
2. one flask at 30degC in water bath shaker
5:00 - Janice - grow up some flaks of 2x80ml of LB with pNIC-Bsa4 in Kanamycin for eventual midiprep
Meet at the lab at 5:30 to head over to Dr. B's house
Will use cars or can also take the #21 Bus that leaves from Dean Keeton & University @ 5:47 pm
The Naturally Obsessed viewing will be Thursday June 28th form 6-7 pm at Dr. B's House
FRIDAY 29-Jun
12:30, 1:00 - all day: protein expression (Max , Kaarthik , Urvashi , Janice , Rishi, Aldo (observe) )
-- we will start a little later than we normally would but we will use an abbreviated induction phase (~ 3 hrs) so that we can finish in a more reasonable time.
Monitor log phase growth in Excel spreadsheet graph
Janice - spin down pNIC-Bsa4 pellets. Save for doing Midiprep next week
Make Protein Gels (Homemade SDS-Page) with Dr. B or Joey - Alex, Michael
------------------------------------- (and if time permits: Max, Kaarthik, Uvashi, Janice, Rishi, Aldo)
High Schoolers and new guys
pmCherry PCR
pLIC PCR
EVERYONE: determine gene inside pNIC-Bsa4 by checking your pLIC sequencing that you sent to the core the other week
SATURDAY 30-Jun
SUNDAY 1-Jul
(NOT YET) ProtocolBacterialGrowthCurve_VDS_Summ12.xlsx - test (needs to be modified a little)
FRIDAY 21-May
SATURDAY 22-May
SUNDAY 23-May
MONDAY 24-May
TUESDAY 25-May
6th Week
MONDAY 2-JulEVERYONE: determine gene inside pNIC-Bsa4 by checking your pLIC sequencing that you sent to the core the other week
EVERYONE THAT HAS DONE MIDI-Prep (successfully): Have you submitted your sample to sequencing? Does it turn out to be the right plasmid?
Veteran VDSers - work on cloning
Daniel & Andrew - do test growth of FtHAP and MtPSTP in 50 ml of LB + Kan
Each Person:
- one flask at 30degC in water bath shaker
- one flask at 37deg in air incubator
Measure OD every few hours over ~ 8hrs time span until OD reaches 1.000 at 600nmMake LB and Autoclave with flasks that you will use.
------- put 500ml into in 2x 2L flasks
------ put 50 ml into 4 x 250 ml flasks
2:30 - Lab Group Meeting/Journal Club (in WELCH classroom)
High Schoolers and new guys (Rishi,Faiz, Priya, Bobbi, Paul):
--ProtocolPrimerDilutionVDS_Summ12.docx
--pmCherry PCR
--pLIC PCR - ProtocolPCR_pLICsequencing.xls
--Overlap PCR of target
Janice - overnight growth of 2x 80ml of LB with pNIC-Bsa4 colonies for doing Midiprep
Make Protein Gels (Homemade SDS-Page) with Dr. B or Joey - Alex, Michael
------------------------------------- (and if time permits: Max, Kaarthik, Uvashi, Janice, Rishi, Aldo
TUESDAY 3-Jul
Janice - spin down samples for pNIC-Bsa4 Midiprep
Protein Sonication (Andrew, Alex, Michael, Daniel)
Protein expression - AGAIN
- Joey & Christina's Francisella HAP enzyme
- Sadhana's M. tuberculosis enzyme
Monitor log phase growth in Excel spreadsheet graphmake SDS-Page protein gels for characterization step
3:00 - Algae Lab Tour: Meet in PAI 2.14 - then will walk over to BIO 320
Janice and Sam - Midiprep pNIC-Bsa4 plasmid samples, Nanodrop them and then send to sequencing
WEDNESDAY 4-Jul
OFF - Independence Day
THURSDAY 5-Jul
EVERYONE: determine gene inside pNIC-Bsa4 by checking your pLIC sequencing that you sent to the core the other week
EVERYONE THAT HAS DONE MIDI-Prep (successfully): Have you submitted your sample to sequencing? Does it turn out to be the right plasmid?
~ 10:00 Prep Starter Culture (grow until ~ 8hrs to OD600 = 1 )
- Max - MtPSTP (Sadhana's Tuberculosis)
- Urvashi - MtPSTP (Sadhana's Tuberculosis)
- Kaarthik - FtHAP (Joey's and Christina's Francisella)
- Janice - FtHAP (Joey's and Christina's Francisella)
- Aldo- FtHAP (Joey's and Christina's Francisella)
Protein Expression People also make LB media and autoclaveProtein Sonication (Andrew, Alex, Michael, Daniel)
Janice and Sam - send Midiprep sample of pNIC-Bsa4 to sequencing
~ 6:00 Move Starter Cultureto store in 4degC
FRIDAY 6-Jul
Protein Purification (Andrew, Alex, Michael, Daniel)
--- Run gels, stain and destain
Protein expression 11:00 ? - talk to Dr. B if you can't make this time
make SDS-Page protein gels for characterization step
SATURDAY 7-Jul
SUNDAY 8-Jul
WEDNESDAY 26-May
THURSDAY 27-May
FRIDAY 28-May
TACC Tour - Thursday July 12th @3:00
(meet in lab before - then we'll catch bus up to Pickle campus)Fill out - Medical Waiver
Fill out - Liability form
MONDAY 9-Jul
~ 10:00 Prep Starter Culture (grow until ~ 8hrs to OD600 = 1 )
2:30 - Lab Group Meeting/Journal Club (in WELCH classroom)
~ 6:00 Move Starter Cultureto store in 4degC
TUESDAY 10-Jul
Protein expression 11:00 ? -
WEDNESDAY 11-Jul
NOTE - not change in schedule
TACC Tour at VisLab in ACES building ON CAMPUS - @3:00
(meet in lab before at 2:50to walk over)THURSDAY 12-Jul
TACC Tour - @3:00 Cancelled and moved to WED
(meet in lab before - then we'll catch bus up to Pickle campus)FRIDAY 13-Jul
SATURDAY 14-Jul
SUNDAY 15-Jul
MONDAY 16-Jul
2:30 - Lab Group Meeting/Journal Club (in WELCH classroom)
TUESDAY 17-Jul
WEDNESDAY 18-Jul
THURSDAY 19-Jul
FRIDAY 20-Jul
SATURDAY 21-Jul
SUNDAY 22-Jul
MONDAY 23-Jul
2:30 - Lab Group Meeting/Journal Club (in WELCH classroom)
TUESDAY 24-Jul
WEDNESDAY 25-Jul
2-4 pm - Middle Schoolers visit lab
THURSDAY 26-Jul
072612 - Thursday 3:00 - GASF (Genome Sequencing and Analysis Facility) Tour in MBB 4.102
Paper to read before the tour: NGS_Mardis.pdf
–Meet in lab at 2:50
FRIDAY 27-Jul
SATURDAY 28-Jul
SUNDAY 29-Jul
SATURDAY 29-May
SUNDAY 30-May
MONDAY 31-May
TUESDAY 1-Jun
WEDNESDAY 2-Jun
THURSDAY 3-Jun
FRIDAY 4-Jun
SATURDAY 5-Jun
SUNDAY 6-Jun
MONDAY 7-Jun
TUESDAY 8-Jun
WEDNESDAY 9-Jun
THURSDAY 10-Jun
FRIDAY 11-Jun
SATURDAY 12-Jun
SUNDAY 13-Jun
MONDAY 14-Jun
TUESDAY 15-Jun
WEDNESDAY 16-Jun
THURSDAY 17-Jun
FRIDAY 18-Jun
SATURDAY 19-Jun
SUNDAY 20-Jun
MONDAY 21-Jun
TUESDAY 22-Jun
WEDNESDAY 23-Jun
THURSDAY 24-Jun
FRIDAY 25-Jun
SATURDAY 26-Jun
SUNDAY 27-Jun
MONDAY 28-Jun
TUESDAY 29-Jun
WEDNESDAY 30-Jun
THURSDAY 1-Jul
FRIDAY 2-Jul
SATURDAY 3-Jul
SUNDAY 4-Jul
MONDAY 5-Jul
TUESDAY 6-Jul
WEDNESDAY 7-Jul
THURSDAY 8-Jul
FRIDAY 9-Jul
SATURDAY 10-Jul
SUNDAY 11-Jul
MONDAY 12-Jul
TUESDAY 13-Jul
WEDNESDAY 14-Jul
THURSDAY 15-Jul
FRIDAY 16-Jul
SATURDAY 17-Jul
SUNDAY 18-Jul
MONDAY 19-Jul
TUESDAY 20-Jul
WEDNESDAY 21-Jul
THURSDAY 22-Jul
FRIDAY 23-Jul
SATURDAY 24-Jul
SUNDAY 25-Jul
MONDAY 26-Jul
TUESDAY 27-Jul
WEDNESDAY 28-Jul
THURSDAY 29-Jul
FRIDAY 30-Jul
SATURDAY 31-Jul
SUNDAY 1-Aug
MONDAY 2-Aug
TUESDAY 3-Aug
WEDNESDAY 4-Aug
THURSDAY 5-Aug
FRIDAY 6-Aug
SATURDAY 7-Aug
SUNDAY 8-Aug